Communicating imaging findings in peritoneal mesothelioma: the impact of 'PAUSE' on surgical decision-making

The peritoneal cavity is the second commonest site of mesothelioma after the pleural cavity. There are five histological types of peritoneal mesothelioma with variable symptomatology, clinical presentation and prognosis. Cystic mesothelioma is a borderline malignant neoplasm with a favourable prognosis, well-differentiated papillary mesothelioma is generally a low-grade malignancy, and all other varieties such as epithelioid, sarcomatoid and biphasic mesothelioma are highly malignant types of peritoneal mesothelioma with poor prognosis. Malignant peritoneal mesothelioma was considered inevitably fatal prior to the introduction of cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) in selected cases where long-term survival and cure could be achieved. However, the survival benefits following CRS and HIPEC mainly depend on completeness of cytoreduction, which come at the cost of high morbidity and potential mortality. Using the acronym 'PAUSE', we aimed at describing the key imaging findings that impact surgical decision-making in patients with peritoneal mesothelioma. PAUSE stands for peritoneal cancer index, ascites and abdominal wall disease, unfavourable sites of involvement, small bowel and mesenteric disease and extraperitoneal disease. Reporting components of 'PAUSE' is crucial for patient selection. Despite limitations of CT in accurately depicting the volume of disease, describing findings in terms of PAUSE plays an important role in excluding patients who might not benefit from CRS and HIPEC.

Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes

Next-generation DNA sequencing (NGS) technologies have made generating genomic sequence for organisms of interest affordable and commonplace. However, NGS platforms and analysis software are generally tuned to be used on large and complex genomes or metagenomic samples. Determining the complete genome sequence of a single bacteriophage requires a somewhat different perspective, workflow, and sensitivity to the nature of phages. Because phage genomes consist of mostly coding regions (see Pope/Jacobs-Sera chapter), a very high standard should be adopted when completing these genomes so that the subsequent steps of annotation and analysis are not sabotaged by sequencing errors. While read quality and assembly algorithms have continued to improve, achieving this standard still requires a significant amount of human oversight and expertise. This chapter describes our workflow for sequencing, assembling, and finishing phage genomes to a high standard by the NGS platforms Illumina, Ion Torrent, and 454.